Abstract:
Archaea is a group of single-cell, microscopic organisms that have no nucleus or other membrane-bound organelles. They have many similar structural and metabolic features with bacteria, but they also have several critical differences. Many archaea and bacteria have a syntrophic relationship where they coexist and benefit each other in floc particles, biofilm, and sludge. Archaea that survive in low pH conditions are known as acidophiles, while those that survive in high pH conditions are known as alkalophiles. Sulfolobus is an example of an archaea that prefers high temperatures and extremely low pH. There are two major archaeal kingdoms with species that contribute to the stabilization of wastes: Crenarchaeota and Euryarchaeota. Crenarchaeota contains thermophilic organisms, acidophilic organisms, and ammonia-oxidizing archaea. Euryarchaeota contains halophilic organisms, thermophilic organisms, and methanogens. Archaea also have novel enzymes and metabolic pathways including sulfur pathways involved in a variety of dissimilatory and assimilatory forms of sulfur metabolism.Keywords:
Crenarchaeota
Euryarchaeota
Thaumarchaeota
The phylogenetic diversity of archaeal 16S rRNA genes in a thermoacidic spring field of Ohwakudani, Hakone, Japan, was investigated by PCR-based analysis using a novel Archaea-specific primer designed in the present study. Clone libraries of archaeal 16S rRNA genes were constructed from hot water (78°C) and mud (28°C) samples by PCR using a newly designed forward primer and a previously reported forward primer with reverse primers. Most phylotypes found in the libraries from the hot water sample were related to cultured (hyper)thermophiles. The phylotypes and their detection frequencies from the hot water sample were similar for the libraries amplified with the two different primer sets. In contrast, phylotypes having a low similarity (<95%) to cultured Archaea were found in the libraries from the mud sample. Some of the phylotypes were relatively close to members of Thermoplasmata (80–93% similarity) and the others were not clearly affiliated with Crenarchaeota and Euryarchaeota, but related to Thaumarchaeota and Korarchaeota. The phylotypes and their detection frequencies were significantly different between the two libraries of the mud sample. Our results from the PCR-based analysis using the redesigned primer suggest that more diverse, uncultured Archaea are present in acidic environments at a low temperature than previously recognized.
Phylotype
Crenarchaeota
Thaumarchaeota
Euryarchaeota
Primer (cosmetics)
Library
Hot spring
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Citations (49)
Abstract Archaea plays an important role in biogeochemical processes. Using the quantitative polymerase chain reaction (qPCR) and Illumina high-throughput sequencing, eight sediment samples collected in Liaohe Estuary were used to investigate the effects of salinity gradient on the archaeal community structure and ecological functions. The results showed that archaeal abundance ranged from 5.1 × 10 5 to 1.3 × 10 6 copies/g. Archaeal community included the classes of Thaumarchaeota (69%), Euryarchaeota (29%), and Crenarchaeota (0.01%), respectively. Methanogens in the genera Methanococcoides, Methanoregula , and Methanosaeta and Marine Group I, Candidatus Nitrososphaera , and Nitrososphaera within the ammonia-oxidizing archaea were abundant in freshwater sediments, whereas Marine Benthic Group B and Marine Benthic Group D were abundant in seawater sediments. The positive correlation was observed in between the abundances of Euryarchaeota and salinities (P < 0.05). Physico-chemical analysis in the sediments showed that the temperature and salinity were impacted on the abundance and distribution of archaea significantly (P < 0.05). In general, these results have broadened our understanding on the changes of the archaeal abundance and community structure in estuarine sediment along the salinity gradient.
Crenarchaeota
Thaumarchaeota
Euryarchaeota
Biogeochemical Cycle
Methanosaeta
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Citations (5)
In the present study, we used culture-independent methods to investigate the diversity of methanogenic archaea and their distribution in five permafrost samples collected from a borehole in the Kolyma River Lowland (north-east of Russia). Total DNA was extracted from methane-containing permafrost samples of different age and amplified by PCR. The resulting DNA fragments were cloned. Phylogenetic analysis of the sequences showed the presence of archaea in all studied samples; 60%–95% of sequences belonged to the Euryarchaeota. Methanogenic archaea were novel representatives of Methanosarcinales, Methanomicrobiales, Methanobacteriales and Methanocellales orders. Bathyarchaeota (Miscellaneous Crenarchaeota Group) representatives were found among nonmethanogenic archaea in all the samples studied. The Thaumarchaeota representatives were not found in the upper sample, whereas Woesearchaeota (formerly DHVEG-6) were found in the three deepest samples. Unexpectedly, the greatest diversity of archaea was observed at a depth of 22.3 m, probably due to the availability of the labile organic carbon and/or due to the migration of the microbial cells during the freezing front towards the bottom.
Crenarchaeota
Thaumarchaeota
Euryarchaeota
Methanomicrobiales
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Citations (42)
Using massively parallel sequencing (the Roche 454 platform) we have studied the diversity of archaeal 16S rRNA gene sequences in oxic and anoxic sediments at six sites in Lake Baikal with oil- and gas-bearing fluids discharge. Archaeal communities appeared to be represented mainly by five phyla: Euryarchaeota, Crenarchaeota, Thaumarchaeota, Bathyarchaeota (miscellaneous Crenarchaeotic group), and Woesearchaeota (deep sea hydrothermal vent group 6). Among them we detected sequences of methanogens of the orders Methanomicrobiales, Methanosarsinales, Methanococcales, as well as representatives of the following uncultured archaeal lineages: Group C3, Marine Benthic Group D, and Terrestrial Miscellaneous Group. We have also identified sequences of ammonia-oxidizing archaea of the phyla Crenarchaeota and Thaumarchaeota. Phylogenetic analysis showed the presence ANME-2d-related sequences. However, the analysis of mcrA genes libraries has not revealed typical representatives of ANME groups. Comparison of amplicon libraries 16S rRNA gene fragments from different samples proved the widespread presence of previously detected Baikal archaeal lineages, which are members of the phylum Crenarchaeota and Thaumarchaeota (formerly Group C3 of Crenarchaeota).
Crenarchaeota
Thaumarchaeota
Euryarchaeota
Methanomicrobiales
Operational taxonomic unit
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Citations (19)
Significance An archaeal origin for eukaryotes is an exciting recent finding. Nevertheless, it has been based largely on the reconstruction of universal trees. The use of an alternative strategy based on markers shared between Archaea and eukaryotes and Archaea and Bacteria bypasses potential problems linked to the analysis of the three domains simultaneously. Comparison of the phylogenies obtained by these two complementary sets of markers supports a sister relationship between eukaryotes and the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota lineage but also robustly indicates a root of the tree of Archaea that challenges the traditional topology of this domain. This sensibly changes our perspective of the ancient evolution of the Archaea, early life, and Earth.
Crenarchaeota
Euryarchaeota
Thaumarchaeota
Lineage (genetic)
Three-domain system
Taxonomic rank
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Euryarchaeota
Thaumarchaeota
Crenarchaeota
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Thaumarchaeota
Crenarchaeota
Euryarchaeota
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Citations (456)
Thaumarchaeota
Crenarchaeota
Euryarchaeota
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Using a polyphasic approach, we examined the presence of Archaea in the Gulf of Aqaba, a warm marine ecosystem, isolated from major ocean currents and subject to pronounced seasonal changes in hydrography. Catalyzed reported deposition FISH analyses showed that Archaea make up to >20% of the prokaryotic community in the Gulf. A spatial separation between the two major phyla of Archaea was observed during summer stratification. Euryarchaeota were found exclusively in the upper 200 m, whereas Crenarchaeota were present in greater numbers in layers below the summer thermocline. 16S rRNA gene-based denaturing gradient gel electrophoresis confirmed this depth partitioning and revealed further diversity of Crenarchaeota and Euryarchaeota populations along depth profiles. Phylogenetic analysis showed pelagic Crenarchaeota and Euryarchaeota to differ from coral-associated Archaea from the Gulf, forming distinct clusters within the Marine Archaea Groups I and II. Endsequencing of fosmid libraries of environmental DNA provided a tentative identification of some members of the archaeal community and their role in the microbial community of the Gulf. Incorporation studies of radiolabeled leucine and bicarbonate in the presence of different inhibitors suggest that the archaeal community participates in autotrophic CO(2) uptake and contributes little to the heterotrophic activity.
Crenarchaeota
Euryarchaeota
Thaumarchaeota
Mesopelagic zone
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Citations (33)
Significance CO 2 fixation is the most important biosynthesis process on Earth, enabling autotrophic organisms to synthesize their entire biomass from inorganic carbon at the expense of energy generated by photo- or chemotrophic processes. In the present study we demonstrate an autotrophy pathway that represents the most energy-efficient mechanism for fixing inorganic carbon in the presence of oxygen. This novel variant of the hydroxypropionate/hydroxybutyrate cycle appears to be common in a ubiquitous and abundant group of microorganisms that can thrive in nutrient-limited environments. This discovery offers a biochemical explanation for the remarkable ecological success of the ammonia-oxidizing archaea in extremely nutrient-limited environments typical of most of the open ocean.
Thaumarchaeota
Crenarchaeota
Autotroph
Euryarchaeota
Carbon fixation
Nitrogen Cycle
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Citations (426)